Starting phenix.real_space_refine on Tue Aug 4 18:28:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooy_17033/08_2026/8ooy_17033.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 3520 2.51 5 N 1029 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4782 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 575} Chain: "T" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.45, per 1000 atoms: 0.25 Number of scatterers: 5828 At special positions: 0 Unit cell: (89.452, 96.14, 78.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 51 15.00 Mg 1 11.99 O 1212 8.00 N 1029 7.00 C 3520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 322.1 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 62.7% alpha, 5.6% beta 23 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.673A pdb=" N LYS A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.604A pdb=" N LEU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.605A pdb=" N ASP A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.944A pdb=" N GLU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.045A pdb=" N ILE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.647A pdb=" N GLN A 488 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 519 Proline residue: A 514 - end of helix removed outlier: 3.555A pdb=" N HIS A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 532 through 544 removed outlier: 4.405A pdb=" N VAL A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.831A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.628A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.032A pdb=" N LYS A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 636 " --> pdb=" O GLY A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.799A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 removed outlier: 3.877A pdb=" N ILE A 679 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 745 through 749 Processing helix chain 'A' and resid 750 through 767 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 795 through 812 removed outlier: 3.734A pdb=" N LEU A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 871 removed outlier: 3.743A pdb=" N ALA A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.570A pdb=" N ALA A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.620A pdb=" N TYR A 382 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 375 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.262A pdb=" N PHE A 352 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS A 416 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.587A pdb=" N SER A 670 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 699 through 702 252 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1534 1.33 - 1.45: 1226 1.45 - 1.57: 3153 1.57 - 1.69: 99 1.69 - 1.81: 29 Bond restraints: 6041 Sorted by residual: bond pdb=" C3' C T 21 " pdb=" C2' C T 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.06e+00 bond pdb=" C3' DG D 12 " pdb=" C2' DG D 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.71e+00 bond pdb=" N VAL A 663 " pdb=" CA VAL A 663 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.48e+00 bond pdb=" C3' G T 17 " pdb=" C2' G T 17 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.91e+00 bond pdb=" N THR A 664 " pdb=" CA THR A 664 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.88e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 7951 1.55 - 3.09: 382 3.09 - 4.64: 45 4.64 - 6.18: 7 6.18 - 7.73: 6 Bond angle restraints: 8391 Sorted by residual: angle pdb=" N3 DT P 10 " pdb=" C4 DT P 10 " pdb=" O4 DT P 10 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT P 8 " pdb=" C4 DT P 8 " pdb=" O4 DT P 8 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 8386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2879 17.28 - 34.57: 390 34.57 - 51.85: 194 51.85 - 69.13: 65 69.13 - 86.41: 7 Dihedral angle restraints: 3535 sinusoidal: 1772 harmonic: 1763 Sorted by residual: dihedral pdb=" CA VAL A 815 " pdb=" C VAL A 815 " pdb=" N GLU A 816 " pdb=" CA GLU A 816 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP A 892 " pdb=" CB ASP A 892 " pdb=" CG ASP A 892 " pdb=" OD1 ASP A 892 " ideal model delta sinusoidal sigma weight residual -30.00 -85.98 55.98 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU A 917 " pdb=" CG GLU A 917 " pdb=" CD GLU A 917 " pdb=" OE1 GLU A 917 " ideal model delta sinusoidal sigma weight residual 0.00 86.41 -86.41 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 3532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 644 0.042 - 0.083: 210 0.083 - 0.125: 81 0.125 - 0.167: 7 0.167 - 0.208: 2 Chirality restraints: 944 Sorted by residual: chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 779 " pdb=" N ILE A 779 " pdb=" C ILE A 779 " pdb=" CB ILE A 779 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 941 not shown) Planarity restraints: 913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 521 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 522 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 779 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 780 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 780 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 780 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 901 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C HIS A 901 " 0.026 2.00e-02 2.50e+03 pdb=" O HIS A 901 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 902 " -0.009 2.00e-02 2.50e+03 ... (remaining 910 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5044 3.17 - 3.75: 10010 3.75 - 4.32: 13143 4.32 - 4.90: 20807 Nonbonded interactions: 49064 Sorted by model distance: nonbonded pdb=" OD1 ASP A 355 " pdb="MG MG A1001 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASN A 524 " pdb=" ND2 ASN A 528 " model vdw 2.201 3.120 nonbonded pdb=" NE2 HIS A 555 " pdb=" OE2 GLU A 685 " model vdw 2.206 3.120 nonbonded pdb=" OE1 GLU A 729 " pdb=" NZ LYS A 731 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 817 " pdb=" OG1 THR A 851 " model vdw 2.231 3.040 ... (remaining 49059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6041 Z= 0.344 Angle : 0.740 7.727 8391 Z= 0.519 Chirality : 0.047 0.208 944 Planarity : 0.004 0.045 913 Dihedral : 20.016 86.412 2395 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.79 % Allowed : 0.39 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.35), residues: 602 helix: 0.59 (0.30), residues: 315 sheet: -3.34 (0.66), residues: 47 loop : -1.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 806 TYR 0.015 0.001 TYR A 814 PHE 0.016 0.002 PHE A 354 TRP 0.006 0.001 TRP A 465 HIS 0.011 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.34 ( 6041) covalent geometry : angle 0.73952 / 0.52 ( 8391) hydrogen bonds : bond 0.14500 / 9.74 ( 311) hydrogen bonds : angle 6.35157 / 4.16 ( 853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 679 ILE cc_start: 0.8365 (mm) cc_final: 0.8088 (mm) REVERT: A 848 MET cc_start: 0.7811 (mmm) cc_final: 0.7189 (mmm) outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.0664 time to fit residues: 7.1142 Evaluate side-chains 53 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.105695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083702 restraints weight = 14687.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084414 restraints weight = 11027.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085356 restraints weight = 8768.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085570 restraints weight = 7036.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085694 restraints weight = 6648.320| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6041 Z= 0.150 Angle : 0.648 8.879 8391 Z= 0.355 Chirality : 0.043 0.190 944 Planarity : 0.005 0.053 913 Dihedral : 21.917 65.329 1200 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.38 % Allowed : 6.69 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.35), residues: 602 helix: 0.71 (0.29), residues: 325 sheet: -3.24 (0.64), residues: 49 loop : -1.54 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 806 TYR 0.020 0.002 TYR A 814 PHE 0.019 0.002 PHE A 886 TRP 0.004 0.001 TRP A 342 HIS 0.008 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 6041) covalent geometry : angle 0.64783 / 0.35 ( 8391) hydrogen bonds : bond 0.04555 / 3.03 ( 311) hydrogen bonds : angle 5.15971 / 3.51 ( 853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8270 (mt) cc_final: 0.7977 (mt) REVERT: A 384 PRO cc_start: 0.8385 (Cg_exo) cc_final: 0.8129 (Cg_endo) REVERT: A 506 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8345 (mm) REVERT: A 848 MET cc_start: 0.7544 (mmm) cc_final: 0.7131 (mmm) outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.0527 time to fit residues: 5.0700 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.0170 chunk 60 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083179 restraints weight = 14604.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083824 restraints weight = 11113.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084755 restraints weight = 9008.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085042 restraints weight = 7152.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085156 restraints weight = 6763.205| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6041 Z= 0.154 Angle : 0.613 7.676 8391 Z= 0.335 Chirality : 0.042 0.158 944 Planarity : 0.005 0.050 913 Dihedral : 21.931 64.573 1200 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.77 % Allowed : 12.01 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.35), residues: 602 helix: 0.82 (0.29), residues: 325 sheet: -3.29 (0.64), residues: 49 loop : -1.46 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 806 TYR 0.020 0.001 TYR A 814 PHE 0.017 0.002 PHE A 886 TRP 0.004 0.001 TRP A 866 HIS 0.006 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6041) covalent geometry : angle 0.61305 / 0.34 ( 8391) hydrogen bonds : bond 0.04184 / 2.77 ( 311) hydrogen bonds : angle 4.89662 / 3.34 ( 853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8374 (mt) cc_final: 0.8101 (mt) REVERT: A 506 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8305 (mm) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.0624 time to fit residues: 5.9318 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 0.0060 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082593 restraints weight = 14755.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082414 restraints weight = 12128.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083482 restraints weight = 9870.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083657 restraints weight = 7757.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083911 restraints weight = 8080.341| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6041 Z= 0.164 Angle : 0.607 7.896 8391 Z= 0.332 Chirality : 0.042 0.185 944 Planarity : 0.005 0.048 913 Dihedral : 22.004 63.471 1200 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.57 % Allowed : 14.17 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.35), residues: 602 helix: 0.83 (0.29), residues: 326 sheet: -3.37 (0.59), residues: 49 loop : -1.44 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 682 TYR 0.020 0.002 TYR A 814 PHE 0.018 0.002 PHE A 792 TRP 0.006 0.001 TRP A 342 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 6041) covalent geometry : angle 0.60710 / 0.33 ( 8391) hydrogen bonds : bond 0.04041 / 2.66 ( 311) hydrogen bonds : angle 4.78903 / 3.26 ( 853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 755 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8218 (ppt170) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.0752 time to fit residues: 6.5871 Evaluate side-chains 58 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 760 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.105582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083031 restraints weight = 14940.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083771 restraints weight = 10527.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084551 restraints weight = 9277.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084907 restraints weight = 7283.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085056 restraints weight = 6814.407| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6041 Z= 0.133 Angle : 0.577 7.984 8391 Z= 0.315 Chirality : 0.041 0.156 944 Planarity : 0.004 0.047 913 Dihedral : 21.991 65.219 1200 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.15 % Allowed : 14.17 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.35), residues: 602 helix: 0.95 (0.29), residues: 326 sheet: -3.19 (0.60), residues: 49 loop : -1.32 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 806 TYR 0.017 0.001 TYR A 814 PHE 0.018 0.002 PHE A 792 TRP 0.006 0.001 TRP A 342 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 6041) covalent geometry : angle 0.57692 / 0.31 ( 8391) hydrogen bonds : bond 0.03736 / 2.48 ( 311) hydrogen bonds : angle 4.60331 / 3.14 ( 853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8330 (mm) REVERT: A 614 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7717 (mm) outliers start: 16 outliers final: 8 residues processed: 74 average time/residue: 0.0740 time to fit residues: 7.5091 Evaluate side-chains 65 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 0.0040 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.105857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084722 restraints weight = 14815.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085068 restraints weight = 12355.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085913 restraints weight = 11117.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086370 restraints weight = 7710.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086504 restraints weight = 7233.630| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6041 Z= 0.128 Angle : 0.592 8.030 8391 Z= 0.321 Chirality : 0.041 0.168 944 Planarity : 0.004 0.048 913 Dihedral : 21.987 66.480 1200 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.76 % Allowed : 15.75 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.35), residues: 602 helix: 0.96 (0.29), residues: 326 sheet: -2.96 (0.61), residues: 48 loop : -1.22 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.016 0.001 TYR A 814 PHE 0.018 0.001 PHE A 886 TRP 0.005 0.001 TRP A 342 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 6041) covalent geometry : angle 0.59214 / 0.32 ( 8391) hydrogen bonds : bond 0.03758 / 2.48 ( 311) hydrogen bonds : angle 4.52238 / 3.10 ( 853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8347 (mm) REVERT: A 614 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7727 (mm) REVERT: A 755 ARG cc_start: 0.8158 (ppt170) cc_final: 0.7766 (ppt170) REVERT: A 788 MET cc_start: 0.7396 (mtm) cc_final: 0.7121 (mtm) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.0696 time to fit residues: 6.9807 Evaluate side-chains 68 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.084250 restraints weight = 14770.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084953 restraints weight = 11596.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085536 restraints weight = 10286.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086115 restraints weight = 7158.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086527 restraints weight = 6433.382| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6041 Z= 0.124 Angle : 0.599 7.990 8391 Z= 0.322 Chirality : 0.041 0.181 944 Planarity : 0.004 0.048 913 Dihedral : 21.970 68.120 1200 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.56 % Allowed : 16.73 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.35), residues: 602 helix: 0.92 (0.29), residues: 328 sheet: -2.82 (0.61), residues: 48 loop : -1.20 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.015 0.001 TYR A 814 PHE 0.016 0.001 PHE A 792 TRP 0.008 0.001 TRP A 342 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 6041) covalent geometry : angle 0.59883 / 0.32 ( 8391) hydrogen bonds : bond 0.03608 / 2.39 ( 311) hydrogen bonds : angle 4.46382 / 3.05 ( 853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8301 (mt) cc_final: 0.7995 (mt) REVERT: A 506 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 614 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7681 (mm) REVERT: A 755 ARG cc_start: 0.8196 (ppt170) cc_final: 0.7817 (ppt170) REVERT: A 788 MET cc_start: 0.7310 (mtm) cc_final: 0.7086 (mtm) outliers start: 13 outliers final: 7 residues processed: 72 average time/residue: 0.0627 time to fit residues: 6.3041 Evaluate side-chains 65 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 905 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 ASN A 761 ASN A 776 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.080662 restraints weight = 14868.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080678 restraints weight = 11929.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081632 restraints weight = 10231.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.081820 restraints weight = 8190.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082300 restraints weight = 7776.690| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6041 Z= 0.267 Angle : 0.724 9.489 8391 Z= 0.382 Chirality : 0.047 0.220 944 Planarity : 0.006 0.046 913 Dihedral : 22.260 73.378 1200 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.74 % Allowed : 16.93 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.34), residues: 602 helix: 0.71 (0.29), residues: 323 sheet: -3.18 (0.54), residues: 53 loop : -1.54 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 682 TYR 0.023 0.003 TYR A 814 PHE 0.016 0.002 PHE A 742 TRP 0.009 0.002 TRP A 465 HIS 0.008 0.002 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.27 ( 6041) covalent geometry : angle 0.72402 / 0.38 ( 8391) hydrogen bonds : bond 0.04907 / 3.23 ( 311) hydrogen bonds : angle 4.84948 / 3.30 ( 853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8358 (mt) cc_final: 0.8079 (mt) REVERT: A 506 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 755 ARG cc_start: 0.8314 (ppt170) cc_final: 0.7820 (ppt170) REVERT: A 788 MET cc_start: 0.7462 (mtm) cc_final: 0.7216 (mtm) REVERT: A 851 THR cc_start: 0.8848 (m) cc_final: 0.8633 (p) outliers start: 19 outliers final: 13 residues processed: 67 average time/residue: 0.0741 time to fit residues: 6.6871 Evaluate side-chains 63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083256 restraints weight = 14838.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083364 restraints weight = 13236.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084299 restraints weight = 12275.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084760 restraints weight = 8450.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084945 restraints weight = 8194.526| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6041 Z= 0.143 Angle : 0.668 8.826 8391 Z= 0.355 Chirality : 0.043 0.268 944 Planarity : 0.005 0.046 913 Dihedral : 22.155 73.905 1200 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.17 % Allowed : 17.91 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.35), residues: 602 helix: 0.81 (0.29), residues: 326 sheet: -3.09 (0.56), residues: 54 loop : -1.17 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 682 TYR 0.018 0.002 TYR A 814 PHE 0.016 0.002 PHE A 886 TRP 0.005 0.001 TRP A 924 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6041) covalent geometry : angle 0.66753 / 0.36 ( 8391) hydrogen bonds : bond 0.03953 / 2.60 ( 311) hydrogen bonds : angle 4.71350 / 3.22 ( 853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8293 (mt) cc_final: 0.8026 (mt) REVERT: A 506 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 755 ARG cc_start: 0.8225 (ppt170) cc_final: 0.7877 (ppt170) REVERT: A 768 MET cc_start: 0.7704 (ppp) cc_final: 0.7120 (ppp) REVERT: A 788 MET cc_start: 0.7300 (mtm) cc_final: 0.6891 (mtm) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.0753 time to fit residues: 6.5891 Evaluate side-chains 61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.103503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081845 restraints weight = 15029.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082028 restraints weight = 13410.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083023 restraints weight = 10982.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083213 restraints weight = 8408.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083416 restraints weight = 8969.625| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6041 Z= 0.179 Angle : 0.687 13.339 8391 Z= 0.362 Chirality : 0.044 0.205 944 Planarity : 0.005 0.047 913 Dihedral : 22.213 75.143 1200 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.17 % Allowed : 17.52 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.35), residues: 602 helix: 0.83 (0.29), residues: 326 sheet: -2.92 (0.59), residues: 53 loop : -1.23 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.019 0.002 TYR A 814 PHE 0.015 0.002 PHE A 886 TRP 0.004 0.001 TRP A 465 HIS 0.004 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 6041) covalent geometry : angle 0.68739 / 0.36 ( 8391) hydrogen bonds : bond 0.04231 / 2.79 ( 311) hydrogen bonds : angle 4.78780 / 3.26 ( 853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8301 (mt) cc_final: 0.8024 (mt) REVERT: A 506 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8240 (mm) REVERT: A 755 ARG cc_start: 0.8253 (ppt170) cc_final: 0.7850 (ppt170) REVERT: A 788 MET cc_start: 0.7258 (mtm) cc_final: 0.6940 (mtm) REVERT: A 792 PHE cc_start: 0.7689 (m-80) cc_final: 0.7476 (m-80) outliers start: 11 outliers final: 10 residues processed: 61 average time/residue: 0.0758 time to fit residues: 6.3829 Evaluate side-chains 62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 907 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082911 restraints weight = 14762.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083040 restraints weight = 10640.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083983 restraints weight = 9207.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084023 restraints weight = 7245.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084264 restraints weight = 7808.814| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6041 Z= 0.142 Angle : 0.657 12.255 8391 Z= 0.345 Chirality : 0.042 0.198 944 Planarity : 0.005 0.046 913 Dihedral : 22.159 76.072 1200 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.56 % Allowed : 17.32 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.35), residues: 602 helix: 0.93 (0.29), residues: 326 sheet: -2.82 (0.60), residues: 53 loop : -1.03 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 682 TYR 0.016 0.001 TYR A 814 PHE 0.017 0.001 PHE A 886 TRP 0.004 0.001 TRP A 513 HIS 0.003 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 6041) covalent geometry : angle 0.65701 / 0.35 ( 8391) hydrogen bonds : bond 0.03854 / 2.55 ( 311) hydrogen bonds : angle 4.64988 / 3.17 ( 853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 964.37 seconds wall clock time: 17 minutes 19.13 seconds (1039.13 seconds total)